org.utgenome.gwt.utgb.client.bio
Class InfoSilkGenerator

java.lang.Object
  org.utgenome.gwt.utgb.client.bio.GenomeRangeVisitorBase
      org.utgenome.gwt.utgb.client.bio.InfoSilkGenerator

All Implemented Interfaces:

GenomeRangeVisitor

public class InfoSilkGenerator
extends GenomeRangeVisitorBase

Generating read information in Silk format, which is used for displaying mouse over message

Author:

leo

Field Summary

ArrayList<String>

lines

Constructor Summary

InfoSilkGenerator()

Method Summary

void	addLine(String text)
List<String>	getLines()
String	getSilk()
void	visitBEDGene(BEDGene g)
void	visitGap(Gap g)
void	visitGraph(GraphData graph)
void	visitInterval(Interval interval)
void	visitRead(Read r)
void	visitReadCoverage(ReadCoverage readCoverage)
void	visitReadList(ReadList readList)
void	visitSAMRead(SAMRead r)
void	visitSAMReadLight(SAMReadLight r)
void	visitSAMReadPairFragment(SAMReadPairFragment fragment)
void	visitSequence(ReferenceSequence referenceSequence)

Methods inherited from class org.utgenome.gwt.utgb.client.bio.GenomeRangeVisitorBase

visitDefault, visitGene, visitSAMReadPair

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

lines

public ArrayList<String> lines

Constructor Detail

InfoSilkGenerator

public InfoSilkGenerator()

Method Detail

getSilk

public String getSilk()

getLines

public List<String> getLines()

addLine

public void addLine(String text)

visitBEDGene

public void visitBEDGene(BEDGene g)

Specified by:

visitBEDGene in interface GenomeRangeVisitor

Overrides:

visitBEDGene in class GenomeRangeVisitorBase

visitGap

public void visitGap(Gap g)

Specified by:

visitGap in interface GenomeRangeVisitor

Overrides:

visitGap in class GenomeRangeVisitorBase

visitInterval

public void visitInterval(Interval interval)

Specified by:

visitInterval in interface GenomeRangeVisitor

Overrides:

visitInterval in class GenomeRangeVisitorBase

visitRead

public void visitRead(Read r)

Specified by:

visitRead in interface GenomeRangeVisitor

Overrides:

visitRead in class GenomeRangeVisitorBase

visitSAMRead

public void visitSAMRead(SAMRead r)

Specified by:

visitSAMRead in interface GenomeRangeVisitor

Overrides:

visitSAMRead in class GenomeRangeVisitorBase

visitSAMReadLight

public void visitSAMReadLight(SAMReadLight r)

Specified by:

visitSAMReadLight in interface GenomeRangeVisitor

Overrides:

visitSAMReadLight in class GenomeRangeVisitorBase

visitSequence

public void visitSequence(ReferenceSequence referenceSequence)

Specified by:

visitSequence in interface GenomeRangeVisitor

Overrides:

visitSequence in class GenomeRangeVisitorBase

visitReadCoverage

public void visitReadCoverage(ReadCoverage readCoverage)

Specified by:

visitReadCoverage in interface GenomeRangeVisitor

Overrides:

visitReadCoverage in class GenomeRangeVisitorBase

visitSAMReadPairFragment

public void visitSAMReadPairFragment(SAMReadPairFragment fragment)

Specified by:

visitSAMReadPairFragment in interface GenomeRangeVisitor

Overrides:

visitSAMReadPairFragment in class GenomeRangeVisitorBase

visitGraph

public void visitGraph(GraphData graph)

Specified by:

visitGraph in interface GenomeRangeVisitor

Overrides:

visitGraph in class GenomeRangeVisitorBase

visitReadList

public void visitReadList(ReadList readList)

Specified by:

visitReadList in interface GenomeRangeVisitor

Overrides:

visitReadList in class GenomeRangeVisitorBase